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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Adar1 B Cell Conditional Knockout Activated B Cells Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Adar1 B Cell Conditional Knockout Activated B Cells Transcriptomes

PROVIDER: PRJNA807650 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18052083_1.fastq.gz	Fastqsanger.gz
	SRR18052083_2.fastq.gz	Fastqsanger.gz
	SRR18052084_1.fastq.gz	Fastqsanger.gz
	SRR18052084_2.fastq.gz	Fastqsanger.gz
	SRR18052085_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Adar1 B Cell Conditional Knockout Activated B Cells Transcriptomes

Project description:Purpose: to compare the gene expression differences between wild-type activated B cells and Adar1 knockout activated B cells Methods: In vitro activated B cells were sorted using a BD FACSAira sorter, and total RNA was extracted using RNeasy Mini Kit (Qiagen) and poly(A) mRNA was isolated with the poly(A) mRNA Magnetic Isolation Module (NEB). Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on an Illumina Hiseq instrument (Illumina). Sequence reads were filtrated using Cutadapt (V1.9.1), and then mapped to the reference genome sequences (GRCm38.98) using Hisat2 (V2.0.1).

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ADAR1-/- mouse Transcriptomes

Project description:Purpose: The goals of this study are to compare WT and ADAR1 knockout mouse B cell transcriptome profiling (RNA-seq) Methods: Cells are sorted from bone marrow of WT and ADAR1 KO mice and mRNA profiles were generated by deep sequencing using Illumina Hiseq. Results: Using an optimized data analysis workflow, we confirmed over hundrad differential expressed genes by KEGG pathway analysis with 185 up-regulated genes and 136 down-regulated genes. Conclusions: Our study represents the first detailed analysis of B cell mRNA profile from WT and ADAR1 KO mice using RNA-Seq. We conclude that ADAR1 plays important roles during early B cell development.

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Next Generation Sequencing Facilitates Quantitative Analysis of peritoneal macrophages Transcriptomes of Dnmt3a macrophage conditional knockout mouse

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Project description:RNAseq analysis of cell lines with ADAR1-p150 and ADAR1-p110 knock-outs and primary human tissue samples (from GSE57353 and GSE99392 data sets) to identify sites of ADAR1 editing

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ADAR1 regulates melanoma progression via miRNAs biogenesis

Project description:Aberrant RNA-editing was observed in several human tumors, but its significance is mostly unknown. Here we show that ADAR1, a ubiquitous RNA-editing enzyme, is commonly lost in metastatic melanoma cells and specimens. Experimental ADAR1 silencing significantly alters melanoma cell morphology, facilitates proliferation and cell-cycle, and increases the tumorigenicity in-vivo. A series of ADAR1 truncation mutants establishes a novel RNA-editing-independent role for ADAR1 in controlling the nuclear and cytoplasmic processing steps of miRNA biogenesis. Altered expression of ADAR1-controled miRNAs accounts for the observed phenotype. We show that the oncogenic miR-17-5p endogenously regulates ADAR1 expression and that its genomic sequence is frequently amplified in melanoma to overexpress the mature miR-17-5p form. ADAR1 and miR-17-5p are ubiquitously expressed, suggesting the generality of this mechanism. Melanoma cell line expressing low ADAR1 levels (ADAR1-Knockdown) using shRNA technique were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to examine the alterations in the genes and microRNA expression profile in the manipulated cell system, due to ADAR1 possible involvement cancer development. To that end, we selected ADAR1-knockdown (ADAR1-KD) cells that demonstrated an enhanced aggressive phenotype both in vivo and in vitro as compared to the control cells (Control).

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